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- PDB-1oby: Crystal structure of the complex of PDZ2 of syntenin with a synde... -
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Basic information
Entry | Database: PDB / ID: 1oby | ||||||
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Title | Crystal structure of the complex of PDZ2 of syntenin with a syndecan-4 peptide. | ||||||
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![]() | CELL ADHESION / ADHESION-COMPLEX / PDZ DOMAIN / SIGNAL TRANSDUCTION / NUCLEAR PROTEIN | ||||||
Function / homology | ![]() Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / regulation of fibroblast migration / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / interleukin-5 receptor complex / interleukin-5 receptor binding ...Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / regulation of fibroblast migration / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / HS-GAG degradation / inner ear receptor cell stereocilium organization / syndecan binding / Neurofascin interactions / presynapse assembly / neurexin family protein binding / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / costamere / frizzled binding / negative regulation of receptor internalization / protein targeting to membrane / Ephrin signaling / ureteric bud development / RIPK1-mediated regulated necrosis / Syndecan interactions / RSV-host interactions / positive regulation of transforming growth factor beta receptor signaling pathway / thrombospondin receptor activity / growth factor binding / positive regulation of focal adhesion assembly / Respiratory syncytial virus (RSV) attachment and entry / fibronectin binding / positive regulation of epithelial to mesenchymal transition / negative regulation of T cell proliferation / Retinoid metabolism and transport / positive regulation of phosphorylation / positive regulation of stress fiber assembly / cell adhesion molecule binding / protein sequestering activity / regulation of mitotic cell cycle / phosphatidylinositol-4,5-bisphosphate binding / ephrin receptor binding / lysosomal lumen / neural tube closure / Cell surface interactions at the vascular wall / protein kinase C binding / adherens junction / positive regulation of JNK cascade / ionotropic glutamate receptor binding / wound healing / Regulation of necroptotic cell death / Golgi lumen / azurophil granule lumen / extracellular vesicle / melanosome / cell migration / presynapse / actin cytoskeleton organization / positive regulation of cell growth / chemical synaptic transmission / nuclear membrane / Ras protein signal transduction / Attachment and Entry / cytoskeleton / blood microparticle / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S. | ||||||
![]() | ![]() Title: Molecular Roots of Degenerate Specificity in Syntenin'S Pdz2 Domain: Reassessment of the Pdz Recognition Paradigm Authors: Kang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.2 KB | Display | ![]() |
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PDB format | ![]() | 34.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.3 KB | Display | ![]() |
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Full document | ![]() | 450.9 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nteC ![]() 1obxC ![]() 1obzC ![]() 1n99S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 8394.598 Da / Num. of mol.: 2 / Fragment: PDZ2, RESIDUES 197-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 743.761 Da / Num. of mol.: 2 / Fragment: LAST 6 RESIDUES, RESIDUES 193-198 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | MOL_ID 1: FUNCTIONS AS AN ADAPTER PROTEIN. MAY ALSO FUNCTION TO COUPLE SYNDECANS TO CYTOSKELETAL ...MOL_ID 1: FUNCTIONS AS AN ADAPTER PROTEIN. MAY ALSO FUNCTION TO COUPLE SYNDECANS TO CYTOSKELET | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 49.7 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.8 Details: SITTING DROP WITH 0.1 M HEPES, PH 6.8, 1.6 M AMMONIUM SULFATE, 20 MM COCL2, AND 0.2 MGSO4 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 294 K / pH: 6.8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 31, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 46421 / % possible obs: 97.4 % / Redundancy: 3.57 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.86 / % possible all: 83.7 |
Reflection | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 50 Å / Num. obs: 12987 / Num. measured all: 46421 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 83.7 % / Num. unique obs: 1108 / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.86 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1N99 Resolution: 1.85→49.39 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.645 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→49.39 Å
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Refine LS restraints |
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